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      Natural history of a mouse model of X-linked myotubular myopathy

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          ABSTRACT

          X-linked myotubular myopathy (XLMTM) is a severe monogenetic disorder of the skeletal muscle. It is caused by loss-of-expression/function mutations in the myotubularin ( MTM1) gene. Much of what is known about the disease, as well as the treatment strategies, has been uncovered through experimentation in pre-clinical models, particularly the Mtm1 gene knockout mouse line ( Mtm1 KO). Despite this understanding, and the identification of potential therapies, much remains to be understood about XLMTM disease pathomechanisms, and about the normal functions of MTM1 in muscle development. To lay the groundwork for addressing these knowledge gaps, we performed a natural history study of Mtm1 KO mice. This included longitudinal comparative analyses of motor phenotype, transcriptome and proteome profiles, muscle structure and targeted molecular pathways. We identified age-associated changes in gene expression, mitochondrial function, myofiber size and key molecular markers, including DNM2. Importantly, some molecular and histopathologic changes preceded overt phenotypic changes, while others, such as triad structural alternations, occurred coincidentally with the presence of severe weakness. In total, this study provides a comprehensive longitudinal evaluation of the murine XLMTM disease process, and thus provides a critical framework for future investigations.

          Abstract

          Summary: This study provides a comprehensive and longitudinal molecular and phenotypic evaluation of the disease process of X-linked myotubular myopathy (XLMTM) in a murine model.

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          Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

          A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Successful analysis requires the integration of a broad set of current biological databases and the application of a robust analytical pipeline to produce readily interpretable results. Metascape is a web-based portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists. In terms of design features, Metascape combines functional enrichment, interactome analysis, gene annotation, and membership search to leverage over 40 independent knowledgebases within one integrated portal. Additionally, it facilitates comparative analyses of datasets across multiple independent and orthogonal experiments. Metascape provides a significantly simplified user experience through a one-click Express Analysis interface to generate interpretable outputs. Taken together, Metascape is an effective and efficient tool for experimental biologists to comprehensively analyze and interpret OMICs-based studies in the big data era.
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            Global, quantitative and dynamic mapping of protein subcellular localization

            Subcellular localization critically influences protein function, and cells control protein localization to regulate biological processes. We have developed and applied Dynamic Organellar Maps, a proteomic method that allows global mapping of protein translocation events. We initially used maps statically to generate a database with localization and absolute copy number information for over 8700 proteins from HeLa cells, approaching comprehensive coverage. All major organelles were resolved, with exceptional prediction accuracy (estimated at >92%). Combining spatial and abundance information yielded an unprecedented quantitative view of HeLa cell anatomy and organellar composition, at the protein level. We subsequently demonstrated the dynamic capabilities of the approach by capturing translocation events following EGF stimulation, which we integrated into a quantitative model. Dynamic Organellar Maps enable the proteome-wide analysis of physiological protein movements, without requiring any reagents specific to the investigated process, and will thus be widely applicable in cell biology. DOI: http://dx.doi.org/10.7554/eLife.16950.001
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              Mitochondrial DNA copy number in human disease: the more the better?

              Most of the genetic information has been lost or transferred to the nucleus during the evolution of mitochondria. Nevertheless, mitochondria have retained their own genome that is essential for oxidative phosphorylation (OXPHOS). In mammals, a gene‐dense circular mitochondrial DNA (mtDNA) of about 16.5 kb encodes 13 proteins, which constitute only 1% of the mitochondrial proteome. Mammalian mtDNA is present in thousands of copies per cell and mutations often affect only a fraction of them. Most pathogenic human mtDNA mutations are recessive and only cause OXPHOS defects if present above a certain critical threshold. However, emerging evidence strongly suggests that the proportion of mutated mtDNA copies is not the only determinant of disease but that also the absolute copy number matters. In this review, we critically discuss current knowledge of the role of mtDNA copy number regulation in various types of human diseases, including mitochondrial disorders, neurodegenerative disorders and cancer, and during ageing. We also provide an overview of new exciting therapeutic strategies to directly manipulate mtDNA to restore OXPHOS in mitochondrial diseases.
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                Author and article information

                Journal
                Dis Model Mech
                Dis Model Mech
                DMM
                dmm
                Disease Models & Mechanisms
                The Company of Biologists Ltd
                1754-8403
                1754-8411
                1 July 2022
                25 July 2022
                25 July 2022
                : 15
                : 7
                : dmm049342
                Affiliations
                [1 ]Program for Genetics and Genome Biology, The Hospital for Sick Children , 686 Bay Street, Toronto, ON M5G 1X8, Canada
                [2 ]Department of Molecular Genetics, University of Toronto , 1 King's College Circle, Toronto, ON M5S 1A8, Canada
                [3 ]Division of Neurology, The Hospital for Sick Children , 686 Bay Street, Toronto, ON M5G 1X8, Canada
                [4 ]Centre for Computational Medicine, The Hospital for Sick Children , 686 Bay Street, Toronto, ON M5G 1X8, Canada
                [5 ]Paediatrics, University of Toronto , 1 King's College Circle, Toronto, ON M5S 1A8, Canada
                Author notes
                [*]

                These authors contributed equally to this work

                []Author for correspondence ( james.dowling@ 123456sickkids.ca )

                Handling Editor: Monkol Lek

                Author information
                http://orcid.org/0000-0002-6509-7697
                http://orcid.org/0000-0002-3984-4169
                Article
                DMM049342
                10.1242/dmm.049342
                9346535
                35694952
                e085eb78-bf59-4c57-af7f-6a607e5def86
                © 2022. Published by The Company of Biologists Ltd

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.

                History
                : 11 October 2021
                : 6 June 2022
                Funding
                Funded by: Office of Extramural Research, National Institutes of Health, http://dx.doi.org/10.13039/100006955;
                Award ID: R21AR074006
                Funded by: Canadian Institutes of Health Research, http://dx.doi.org/10.13039/501100000024;
                Funded by: Natural Sciences and Engineering Research Council of Canada, http://dx.doi.org/10.13039/501100000038;
                Funded by: Myotubular Trust, http://dx.doi.org/10.13039/501100000658;
                Funded by: Mogford Campbell Family Chair Fund;
                Categories
                Neuromuscular Disease Models
                Resource Article

                Molecular medicine
                mice,myotubularin,myotubular myopathy,muscle disease,natural history
                Molecular medicine
                mice, myotubularin, myotubular myopathy, muscle disease, natural history

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